"As former governor of the reserve bank, Mr Mboweni brings to this position vast experience in areas of finance, economic policy as well as in governance", he said.
But Nene's opponents say he was involved in corrupt deals with the Guptas when he was deputy finance minister and head of the state pension fund.
Nene asked Ramaphosa to relieve him of his duties, the Johannesburg-based Business Day newspaper reported Monday, without saying how it got the information.
Although Nene has since apologised for lying about meeting the Guptas, he made a decision to step down from his role.
"At this point, what we are appealing for is for the commission to be allowed to do its work and make findings, and on the basis of that the president will see what further action is required".
The three Gupta brothers, who are allies of former President Jacob Zuma, were implicated by the former anti-graft ombudsman in influencing government appointments and the award of state contracts - allegations they and Zuma deny.
In the latest flare-up of a widening corruption scandal, South Africa's finance minister has resigned from his cabinet post for failing to disclose his meetings with the controversial Gupta business family.
One common theme that has emerged is visits to the family's sprawling Johannesburg property, which is why there has been public anger regarding Nene's revelations.
In a written letter to Ramaphosa, Malema argued that the country, whose economy is in recession, had very serious challenges that needed a credible finance minister to address them.
"Public servants at all spheres and levels of government will have no obligation to responsibly manage state fiscal resources under a compromised minister of finance".
Zuma has also denied any wrongdoing.
"I can confirm that he has been in engagement with Mr Nene and I can also confirm that there has been correspondence that has been exchanged between them and they have spoken on the phone... so they have had ongoing conversations".
All eyes will now be on a much anticipated announcement by Moody's on SA's sovereign credit rating on Friday, and Mboweni's maiden medium-term budget policy statement in two weeks.
This was the sentiment from the ANC and opposition parties after the news broke that Mboweni would replace former minister, Nhlanhla Nene, as the country's finance minister.
"There are various other sensitive developments around him that render him incapable of being a member of the executive‚" Malema said.
Treasury spokesman Jabulani Sikhakhane referred Reuters to the presidency for comment.
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